11-122184817-A-T

Position:

• chr11-122184817-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527474.5(MIR100HG):​n.899-4419T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,126 control chromosomes in the GnomAD database, including 2,007 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2007 hom., cov: 32)
• Consequence: MIR100HG ENST00000527474.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.347-4419T>A		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.301-4419T>A		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.359-4419T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000533109.6	n.854-4419T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23104 AN: 152008 Hom.: 2011 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 23107 AN: 152126 Hom.: 2007 Cov.: 32 AF XY: 0.155 AC XY: 11558 AN XY: 74354

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0602 Hom.: 62

Bravo AF: 0.159

Asia WGS AF: 0.196 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs683185; hg19: chr11-122055525;